AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene70440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70440.t1 MTR_3g083030 94.268 157 8 1 1 156 75 231 3.13e-107 305
MS.gene70440.t1 MTR_3g083050 94.268 157 8 1 1 156 52 208 1.22e-106 303
MS.gene70440.t1 MTR_3g083080 61.392 158 59 1 1 156 50 207 8.71e-65 197
MS.gene70440.t1 MTR_3g082420 38.182 165 87 4 1 154 61 221 3.04e-29 107
MS.gene70440.t1 MTR_3g082340 38.182 165 87 4 1 154 62 222 5.68e-29 106
MS.gene70440.t1 MTR_3g086030 55.556 81 36 0 1 81 23 103 2.76e-24 92.4
MS.gene70440.t1 MTR_3g083150 42.405 158 81 5 7 155 56 212 3.61e-24 93.6
MS.gene70440.t1 MTR_3g080680 40.854 164 82 6 1 154 40 198 2.00e-21 86.3
MS.gene70440.t1 MTR_3g083100 38.889 126 59 4 48 155 49 174 5.83e-18 76.6
MS.gene70440.t1 MTR_8g461300 36.047 172 83 8 3 154 34 198 1.58e-17 75.9
MS.gene70440.t1 MTR_4g055800 34.752 141 74 5 6 138 143 273 1.55e-13 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCGCTTTATTTACAAGAATA+AGG 0.246265 3.1:+66323095 MS.gene70440:CDS
CGCGCGCATATAAACATAAA+AGG 0.298624 3.1:-66323075 None:intergenic
TTCAGGCCGAAGTCAGGATT+TGG 0.346408 3.1:+66323637 MS.gene70440:CDS
CAATTACAATGCTGAGAATC+AGG 0.359881 3.1:+66323415 MS.gene70440:CDS
ATGGCACACGACTTGATGAT+AGG 0.414244 3.1:-66323672 None:intergenic
AAAGCTATAACAGAGCTGTT+AGG 0.436414 3.1:-66323615 None:intergenic
AGGCGACGATCATCGGTCAT+AGG 0.464071 3.1:-66323359 None:intergenic
AATTTCTTCTTGTGCTTGAA+AGG 0.481365 3.1:-66323592 None:intergenic
GAGACGAAGGCGACGATCAT+CGG 0.531298 3.1:-66323366 None:intergenic
TCAGGAAAATGTGGCGGTGT+CGG 0.534211 3.1:+66323329 MS.gene70440:CDS
GTCTAACGCAAGCTTGCAGA+CGG 0.539023 3.1:-66323393 None:intergenic
GACGATCATCGGTCATAGGA+AGG 0.543064 3.1:-66323355 None:intergenic
CGATCATCGGTCATAGGAAG+GGG 0.552083 3.1:-66323353 None:intergenic
AGGCCGAAGTCAGGATTTGG+AGG 0.559839 3.1:+66323640 MS.gene70440:CDS
GGTAATGTAATAGAAACCAC+CGG 0.562427 3.1:-66323571 None:intergenic
ACGATCATCGGTCATAGGAA+GGG 0.583505 3.1:-66323354 None:intergenic
TAAGGAGATTGAAGTAGCCA+TGG 0.591215 3.1:+66323134 MS.gene70440:CDS
TGCAGACGGGAGTGAGACGA+AGG 0.616805 3.1:-66323379 None:intergenic
AGTCCTCCAAATCCTGACTT+CGG 0.621247 3.1:-66323643 None:intergenic
TCTAACGCAAGCTTGCAGAC+GGG 0.623247 3.1:-66323392 None:intergenic
GCACTCATCATACTCAGCCA+TGG 0.631008 3.1:-66323151 None:intergenic
GTCAAGACAAGCTATAGACC+CGG 0.640044 3.1:+66323552 MS.gene70440:CDS
AAAATCTCAGGAAAATGTGG+CGG 0.681893 3.1:+66323323 MS.gene70440:CDS
GCACACGACTTGATGATAGG+TGG 0.696773 3.1:-66323669 None:intergenic
GTAATGTAATAGAAACCACC+GGG 0.701603 3.1:-66323570 None:intergenic
AAGACAAGCTATAGACCCGG+TGG 0.734466 3.1:+66323555 MS.gene70440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAATTTTAATGATTCATTC+TGG + chr3.1:66323252-66323271 MS.gene70440:intron 15.0%
AATTTCTTCTTGTGCTTGAA+AGG - chr3.1:66323595-66323614 None:intergenic 30.0%
ACGTCAACAAAAACGAAATT+TGG - chr3.1:66323531-66323550 None:intergenic 30.0%
TAGATGAGTTACTTACACTT+AGG - chr3.1:66323185-66323204 None:intergenic 30.0%
! CTCCTTATCTTTTTGAATCT+GGG - chr3.1:66323121-66323140 None:intergenic 30.0%
! TCTCCTTATCTTTTTGAATC+TGG - chr3.1:66323122-66323141 None:intergenic 30.0%
!! GCGCTTTATTTACAAGAATA+AGG + chr3.1:66323095-66323114 MS.gene70440:CDS 30.0%
!! TTTTCCTGAGATTTTTGGAA+CGG - chr3.1:66323318-66323337 None:intergenic 30.0%
AAAATCTCAGGAAAATGTGG+CGG + chr3.1:66323323-66323342 MS.gene70440:CDS 35.0%
AAAGCTATAACAGAGCTGTT+AGG - chr3.1:66323618-66323637 None:intergenic 35.0%
CAATTACAATGCTGAGAATC+AGG + chr3.1:66323415-66323434 MS.gene70440:CDS 35.0%
CCAAAAATCTCAGGAAAATG+TGG + chr3.1:66323320-66323339 MS.gene70440:CDS 35.0%
GGTAATGTAATAGAAACCAC+CGG - chr3.1:66323574-66323593 None:intergenic 35.0%
GTAATGTAATAGAAACCACC+GGG - chr3.1:66323573-66323592 None:intergenic 35.0%
! CCACATTTTCCTGAGATTTT+TGG - chr3.1:66323323-66323342 None:intergenic 35.0%
!!! TTTCCTGAGATTTTTGGAAC+GGG - chr3.1:66323317-66323336 None:intergenic 35.0%
AACACAACACAACACAACAC+AGG + chr3.1:66323277-66323296 MS.gene70440:intron 40.0%
CGCGCGCATATAAACATAAA+AGG - chr3.1:66323078-66323097 None:intergenic 40.0%
GGCCCAGATTCAAAAAGATA+AGG + chr3.1:66323116-66323135 MS.gene70440:CDS 40.0%
TAAGGAGATTGAAGTAGCCA+TGG + chr3.1:66323134-66323153 MS.gene70440:CDS 40.0%
! CAGCTCTGTTATAGCTTTTC+AGG + chr3.1:66323620-66323639 MS.gene70440:CDS 40.0%
!!! TTCCTGAGATTTTTGGAACG+GGG - chr3.1:66323316-66323335 None:intergenic 40.0%
ACGATCATCGGTCATAGGAA+GGG - chr3.1:66323357-66323376 None:intergenic 45.0%
AGTCCTCCAAATCCTGACTT+CGG - chr3.1:66323646-66323665 None:intergenic 45.0%
ATCCCCGTTCCAAAAATCTC+AGG + chr3.1:66323311-66323330 MS.gene70440:CDS 45.0%
GTCAAGACAAGCTATAGACC+CGG + chr3.1:66323552-66323571 MS.gene70440:CDS 45.0%
TACAATGCTGAGAATCAGGC+AGG + chr3.1:66323419-66323438 MS.gene70440:intron 45.0%
! ATGGCACACGACTTGATGAT+AGG - chr3.1:66323675-66323694 None:intergenic 45.0%
!!! ATATACTATTTTTATTTTTT+AGG + chr3.1:66323503-66323522 MS.gene70440:intron 5.0%
!!! TATACTATTTTTATTTTTTA+GGG + chr3.1:66323504-66323523 MS.gene70440:intron 5.0%
AAGACAAGCTATAGACCCGG+TGG + chr3.1:66323555-66323574 MS.gene70440:CDS 50.0%
CGATCATCGGTCATAGGAAG+GGG - chr3.1:66323356-66323375 None:intergenic 50.0%
GACGATCATCGGTCATAGGA+AGG - chr3.1:66323358-66323377 None:intergenic 50.0%
GCACTCATCATACTCAGCCA+TGG - chr3.1:66323154-66323173 None:intergenic 50.0%
GTCTAACGCAAGCTTGCAGA+CGG - chr3.1:66323396-66323415 None:intergenic 50.0%
TCAGGAAAATGTGGCGGTGT+CGG + chr3.1:66323329-66323348 MS.gene70440:CDS 50.0%
TCTAACGCAAGCTTGCAGAC+GGG - chr3.1:66323395-66323414 None:intergenic 50.0%
TTCAGGCCGAAGTCAGGATT+TGG + chr3.1:66323637-66323656 MS.gene70440:CDS 50.0%
! GCACACGACTTGATGATAGG+TGG - chr3.1:66323672-66323691 None:intergenic 50.0%
!! TAGCTTTTCAGGCCGAAGTC+AGG + chr3.1:66323631-66323650 MS.gene70440:CDS 50.0%
AGGCCGAAGTCAGGATTTGG+AGG + chr3.1:66323640-66323659 MS.gene70440:CDS 55.0%
AGGCGACGATCATCGGTCAT+AGG - chr3.1:66323362-66323381 None:intergenic 55.0%
GAGACGAAGGCGACGATCAT+CGG - chr3.1:66323369-66323388 None:intergenic 55.0%
TGCAGACGGGAGTGAGACGA+AGG - chr3.1:66323382-66323401 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 66323039 66323707 66323039 ID=MS.gene70440
chr3.1 mRNA 66323039 66323707 66323039 ID=MS.gene70440.t1;Parent=MS.gene70440
chr3.1 exon 66323039 66323188 66323039 ID=MS.gene70440.t1.exon1;Parent=MS.gene70440.t1
chr3.1 CDS 66323039 66323188 66323039 ID=cds.MS.gene70440.t1;Parent=MS.gene70440.t1
chr3.1 exon 66323299 66323436 66323299 ID=MS.gene70440.t1.exon2;Parent=MS.gene70440.t1
chr3.1 CDS 66323299 66323436 66323299 ID=cds.MS.gene70440.t1;Parent=MS.gene70440.t1
chr3.1 exon 66323525 66323707 66323525 ID=MS.gene70440.t1.exon3;Parent=MS.gene70440.t1
chr3.1 CDS 66323525 66323707 66323525 ID=cds.MS.gene70440.t1;Parent=MS.gene70440.t1
Gene Sequence

>MS.gene70440

ATGAGTGACTTCTCTATGTATGACGATGACATTGAGCCTTTTATGTTTATATGCGCGCGCTTTATTTACAAGAATAAGGCCCAGATTCAAAAAGATAAGGAGATTGAAGTAGCCATGGCTGAGTATGATGAGTGCTCTCGCAACCTAAGTGTAAGTAACTCATCTATCTATTTCAATTTCATCGTCTTGTGTTTCACTCTCTTAATTTTAATTTTAATTTTAATGATTCATTCTGGACAACACAACACAACACAACACAGGTGTTCGATGCTATCCCCGTTCCAAAAATCTCAGGAAAATGTGGCGGTGTCGGTCCCCTTCCTATGACCGATGATCGTCGCCTTCGTCTCACTCCCGTCTGCAAGCTTGCGTTAGACAATTACAATGCTGAGAATCAGGCAGGTTTCAATACTTATGATGATTATAATATGTTTATGTTTATTTATTCATTCATTGATCATCTAATATACTATTTTTATTTTTTAGGGTCCAAATTTCGTTTTTGTTGACGTTGTCAAGACAAGCTATAGACCCGGTGGTTTCTATTACATTACCTTTCAAGCACAAGAAGAAATTCCTAACAGCTCTGTTATAGCTTTTCAGGCCGAAGTCAGGATTTGGAGGACTGAGCCACCTATCATCAAGTCGTGTGCCATTAAAACTACTTAA
Protein sequence

>MS.gene70440.t1

MSDFSMYDDDIEPFMFICARFIYKNKAQIQKDKEIEVAMAEYDECSRNLSVFDAIPVPKISGKCGGVGPLPMTDDRRLRLTPVCKLALDNYNAENQGPNFVFVDVVKTSYRPGGFYYITFQAQEEIPNSSVIAFQAEVRIWRTEPPIIKSCAIKTT